This paper aims to improve a knowledge base of methyl decanoate, a long alkyl-chain biodiesel surrogate fuel gaining popularity in engine combustion research. To this end, a comparative study on diesel and methyl decanoate combustion has been conducted with a focus on high temperature flame structures and soot distributions in an optically accessible single-cylinder light-duty common-rail diesel engine. The in-cylinder pressure trace and apparent heat release rate curves were well matched for both fuels when the same amount of fuel energy was supplied, which confirmed very similar combustion phasing. Planar laser induced fluorescence of hydroxyl radicals (OH-PLIF) and planar laser induced incandescence (PLII) as well as line-of-sight integrated chemiluminescence imaging of cool-flame signals and electronically excited OH (OH*) were performed for various crank angles to capture the temporal and spatial development of diesel and methyl decanoate flames. The results show that both the cool-flame and OH radical signals are higher during methyl decanoate combustion with their wider distributions and larger in-cylinder volume fraction when compared to that of diesel, suggesting enhanced low- and high-temperature reactions due to oxygen in fuel. The oxygenated methyl decanoate with no aromatics in its molecular structure shows a lower soot formation rate than diesel as evidenced by delayed appearance of LII signals and lower overall intensity. This difference is significant even if the lower sooting propensity of methyl decanoate and thus less attenuation in the laser beam is considered. The rate of soot oxidation is also higher for methyl decanoate not only due to oxygen in fuel but also higher OH radicals surrounding smaller soot pockets compared to diesel.